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  <doc>
    <id>3643</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>129</pageFirst>
    <pageLast>138</pageLast>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume>178</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos</title>
    <parentTitle language="eng">Journal of Structural Biology</parentTitle>
    <identifier type="doi">10.1016/j.jsb.2011.12.004</identifier>
    <identifier type="url">http://www.sciencedirect.com/science/article/pii/S1047847711003509</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Britta Weber</author>
    <author>Garrett Greenan</author>
    <author>Steffen Prohaska</author>
    <author>Daniel Baum</author>
    <author>Hans-Christian Hege</author>
    <author>Thomas Müller-Reichert</author>
    <author>Anthony Hyman</author>
    <author>Jean-Marc Verbavatz</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>3681</id>
    <completedYear>2011</completedYear>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1892</pageFirst>
    <pageLast>1901</pageLast>
    <pageNumber/>
    <edition/>
    <issue>12</issue>
    <volume>17</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Tuner: Principled Parameter Finding for Image Segmentation Algorithms Using Visual Response Surface Exploration</title>
    <parentTitle language="eng">IEEE Trans. Vis. Comput. Graph.</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Thomas Torsney-Weir</author>
    <author>Ahmed Saad</author>
    <author>Torsten Möller</author>
    <author>Hans-Christian Hege</author>
    <author>Britta Weber</author>
    <author>Jean-Marc Verbavatz</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5266</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>e113222</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated stitching of microtubule centerlines across serial electron tomograms</title>
    <parentTitle language="eng">PLoS ONE</parentTitle>
    <identifier type="doi">10.1371/journal.pone.0113222</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-52958</enrichment>
    <author>Britta Weber</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Erin M. Tranfield</author>
    <author>Johanna L. Höög</author>
    <author>Daniel Baum</author>
    <author>Claude Antony</author>
    <author>Tony Hyman</author>
    <author>Jean-Marc Verbavatz</author>
    <author>Steffen Prohaska</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5129</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>261</pageFirst>
    <pageLast>278</pageLast>
    <pageNumber>18</pageNumber>
    <edition/>
    <issue/>
    <volume/>
    <type>incollection</type>
    <publisherName>Springer</publisherName>
    <publisherPlace/>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">The Segmentation of Microtubules in Electron Tomograms Using Amira</title>
    <parentTitle language="eng">Mitosis: Methods and Protocols</parentTitle>
    <identifier type="doi">10.1007/978-1-4939-0329-0_12</identifier>
    <enrichment key="Series">Methods in Molecular Biology</enrichment>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Stefanie Redemann</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Britta Weber</author>
    <author>Marit Möller</author>
    <author>Jean-Marc Verbavatz</author>
    <author>Anthony Hyman</author>
    <author>Daniel Baum</author>
    <author>Steffen Prohaska</author>
    <author>Thomas Müller-Reichert</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5295</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2014-10-28</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated stitching of microtubule centerlines across serial electron tomograms</title>
    <abstract language="eng">Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation.  3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts’ opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-52958</identifier>
    <identifier type="doi">10.1371/journal.pone.0113222</identifier>
    <enrichment key="SourceTitle">published in PLoS ONE</enrichment>
    <author>Britta Weber</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Erin M. Tranfield</author>
    <author>Johanna L. Höög</author>
    <author>Daniel Baum</author>
    <author>Claude Antony</author>
    <author>Tony Hyman</author>
    <author>Jean-Marc Verbavatz</author>
    <author>Steffen Prohaska</author>
    <series>
      <title>ZIB-Report</title>
      <number>14-41</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>electron tomography</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>microtubules</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>serial sectioning</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>geometry reconstruction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image and geometry alignment</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>point correspondence</value>
    </subject>
    <collection role="ccs" number="I.4.9">Applications</collection>
    <collection role="ccs" number="">Biology and genetics (REVISED)</collection>
    <collection role="pacs" number="87.17.-d">Cell processes</collection>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="msc" number="92-XX">BIOLOGY AND OTHER NATURAL SCIENCES</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5295/zibreport-14-41_v1.pdf</file>
  </doc>
</export-example>
